It's been years since I've even really thought about the Pokemon fics that I truly enjoyed. I mean, there are quite a few, but I'll narrow it down to the earlier ones that introduced me not only to the Pokemon fandom, but also to long-lasting friendships.
Also, most of these links are from SPPf, since that's the only forum that has most of these stories.
The Ties That Bind - Saffire Persian
This was the fic that introduced me to second-person point-of-view in general. The story's an emotional one, and the second-person just adds to it.
Actually, read anything by Saff. I highly recommend
Metamorphosis.
The Pokemon Rebellion - Typhlogirl
Goodness, this fic. This was the one that finally made me sign up for my first Pokemon forum to leave a review for it. If it wasn't for this fic, I wouldn't be here today, most likely.
It takes the typical "Pokemon are tired of humans" plot and turns it into an amazing story of friendship. And now I want to read it again.
The Legendarian Chronicles - Chibi Pika
Seconding the recommendation for this. It's been a long while since I read it, but it does show how good a OT fic can be.
I'm sure that there are plenty more Pokemon fanfics out there that I can recommend. It's just that two years out of reading Pokemon fanfics and moving computers three times means that I lost a lot of links.
I do have some from different fandoms.
:D? - aramleys_words (on LiveJournal)
It's a Supernatural fic, but you don't need to watch the show to understand it. Just read it. It's amazing and hilarious, and proves that you can use text speak in fics.
Friendship Is Magic Part 1 Script - Louis Baldament (on Google Docs)
Anyone thinking of doing a script fic
needs to look at this one. That is all. It's an fan-written transcript of the first episode for My Little Pony: Friendship is Magic.